From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 08 2012 - 03:48:48 CST

Right, thank you.

rdparm XXX.prmtop

rdparm menu: bonds :RESIDOFINTEREST

actually shows all the bonds that I had set in.

Does VMD require a special command to also show these bonds? By simply
selecting the specific residues (new residues), the bonds confirmed by
rdparm are not seen. I am interested to also see the bonds
graphically.

thanks

francesco

On Thu, Mar 8, 2012 at 9:42 AM, Lorenzo Gontrani <l.gontrani_at_caspur.it> wrote:
> Why don't you check the topology with rdparm (and its "bonds" command)?
>
> Lorenzo Gontrani
>
> 2012/3/8 Francesco Pietra <chiendarret_at_gmail.com>:
>> Hello
>>
>> Bonds were set in xleap (ambertools 1.5), between newly created
>> residues, with command:
>>
>> bond unitname.residuenumber1.atomnameX     unitname.residuenumber2.atomnameY
>>
>>  "check unitname" after each "bond" command revealed some contac
>> between certain atoms. Bond/angle parameters and unit OK. The log file
>> (verbosity 2) does not reveal anomalies. All involved residues are in
>> the same unit.
>>
>> When the obtained top/crd file are loaded to VMD, the bonds, set as
>> above indicated, are not seen, i.e., the two indicated atoms are not
>> connected by a line.
>>
>> What should I further check to check whether the bonds were established or not?
>>
>> thanks
>>
>> francesco pietra
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> =======================================
>  Lorenzo Gontrani
>  Research associate of EDXD group
>  University of Rome "La Sapienza"
>
>  GSM +39 338 7615798
>  Email l DOT gontrani AT caspur DOT it
>  Webpage: http://webcaminiti/gontrani.html
>  =======================================
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber